Smcr8 (Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)) - Rat Genome Database

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Gene: Smcr8 (Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)) Mus musculus
Analyze
Symbol: Smcr8
Name: Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)
RGD ID: 1614898
MGI Page MGI
Description: Predicted to enable protein kinase binding activity and protein kinase inhibitor activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Involved in regulation of autophagy. Located in cytoplasm; postsynapse; and presynapse. Orthologous to human SMCR8 (SMCR8-C9orf72 complex subunit).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2310076G09Rik; AI642055; D030073L15Rik; guanine nucleotide exchange protein SMCR8; MGC103295; Smith-Magenis syndrome chromosomal region candidate gene 8 protein homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,668,351 - 60,679,113 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,668,350 - 60,679,113 (+)EnsemblGRCm39 Ensembl
GRCm381160,777,525 - 60,788,287 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,777,524 - 60,788,287 (+)EnsemblGRCm38mm10GRCm38
MGSCv371160,591,027 - 60,601,789 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361160,593,737 - 60,597,262 (+)NCBIMGSCv36mm8
MGSCv361161,208,627 - 61,212,152 (+)NCBIMGSCv36mm8
Cytogenetic Map11B2NCBI
cM Map1137.83NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11125038   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:15782199   PMID:16141072   PMID:16141073   PMID:17273973  
PMID:18287559   PMID:18799693   PMID:21267068   PMID:21873635   PMID:27103069   PMID:27617292   PMID:27875531   PMID:29950492   PMID:30442666   PMID:30696333   PMID:31625563   PMID:31651360  
PMID:31847700   PMID:32554809   PMID:38064514  


Genomics

Comparative Map Data
Smcr8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391160,668,351 - 60,679,113 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1160,668,350 - 60,679,113 (+)EnsemblGRCm39 Ensembl
GRCm381160,777,525 - 60,788,287 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1160,777,524 - 60,788,287 (+)EnsemblGRCm38mm10GRCm38
MGSCv371160,591,027 - 60,601,789 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361160,593,737 - 60,597,262 (+)NCBIMGSCv36mm8
MGSCv361161,208,627 - 61,212,152 (+)NCBIMGSCv36mm8
Cytogenetic Map11B2NCBI
cM Map1137.83NCBI
SMCR8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381718,315,293 - 18,328,056 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1718,315,293 - 18,328,056 (+)EnsemblGRCh38hg38GRCh38
GRCh371718,218,607 - 18,231,370 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361718,159,319 - 18,172,095 (+)NCBINCBI36Build 36hg18NCBI36
Build 341718,159,440 - 18,167,109NCBI
Celera1719,159,665 - 19,172,441 (+)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1717,972,126 - 17,984,902 (+)NCBIHuRef
CHM1_11718,227,353 - 18,240,129 (+)NCBICHM1_1
T2T-CHM13v2.01718,262,099 - 18,274,862 (+)NCBIT2T-CHM13v2.0
Smcr8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81045,957,146 - 45,968,388 (+)NCBIGRCr8
mRatBN7.21045,457,962 - 45,465,101 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1045,457,605 - 45,468,876 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1050,159,207 - 50,166,360 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01049,649,603 - 49,656,756 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01045,153,192 - 45,160,345 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01047,019,326 - 47,026,465 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1047,018,974 - 47,026,465 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01046,791,502 - 46,798,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41046,924,224 - 46,931,363 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1044,712,528 - 44,719,666 (+)NCBICelera
Cytogenetic Map10q22NCBI
Smcr8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547811,002,174 - 11,015,123 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547811,002,174 - 11,015,123 (-)NCBIChiLan1.0ChiLan1.0
SMCR8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21952,939,905 - 52,952,684 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11757,651,042 - 57,663,823 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01732,858,205 - 32,871,132 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11737,884,037 - 37,897,031 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1737,884,037 - 37,896,972 (-)Ensemblpanpan1.1panPan2
SMCR8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ROS_Cfam_1.0541,356,732 - 41,369,920 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl541,361,422 - 41,369,287 (-)EnsemblROS_Cfam_1.0 Ensembl
Smcr8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560261,018,506 - 61,028,302 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367411,838,834 - 1,844,459 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367411,838,974 - 1,848,742 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMCR8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1260,435,273 - 60,443,520 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11260,435,276 - 60,443,525 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SMCR8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11617,358,952 - 17,367,323 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1617,359,577 - 17,366,851 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660593,537,962 - 3,546,697 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smcr8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248493,149,121 - 3,159,273 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248493,147,251 - 3,159,358 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smcr8
461 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1831
Count of miRNA genes:759
Interacting mature miRNAs:1005
Transcripts:ENSMUST00000056907, ENSMUST00000102667
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357844Si5lq5_mserum IGFBP-5 level QTL 5 (mouse)Not determined112816587362165976Mouse
4141367Inf1_macute ozone induced inflammation (mouse)Not determined44630038113058009Mouse
1357720Kidpq1_mkidney weight percentage QTL 1 (mouse)Not determined111226863768500330Mouse
4141875Etax9_methanol induced ataxia 9 (mouse)Not determined5528498572209927Mouse
1300765Bbaa4_mB.burgdorferi-associated arthritis 4 (mouse)Not determined114618516780185262Mouse
1357851Scfq3_msubcutaneous fat pad weight QTL 3 (mouse)Not determined111226863768500330Mouse
1301788Lbw8_mlupus NZB x NZW 8 (mouse)Not determined113650328770509492Mouse
27226762Feml21_mfemur length 21, 16 week (mouse)111175000065990826Mouse
1302021Nidd1n_mnon-insulin-dependent diabetes mellitus 1 in NSY (mouse)Not determined114516587379978324Mouse
4142121Tmc1m2_mTmc1 modifier 2 (mouse)Not determined1156864027114157957Mouse
1301896Tria1_mT-cell receptor induced activation 1 (mouse)Not determined113661356570613855Mouse
4141470Egq4_mearly growth QTL 4 (mouse)Not determined1226863768500330Mouse
1301426Desp2_mdespair 2 (mouse)Not determined112870858162708700Mouse
4141982Skts-fp2_mskin tumor susceptibility in FVB and PWK 2 (mouse)Not determined5871926685066529Mouse
4142109W10q2_mweight 10 weeks QTL 2 (mouse)Not determined1226863768500330Mouse
4141853Skmw17_mskeletal muscle weight 17 (mouse)Not determined113708094171081064Mouse
1357878Mastr_mmodifier of astrocytoma (mouse)Not determined114570858189818733Mouse
4141084Spqq1_msperm quality QTL 1 (mouse)Not determined5406567063319522Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13524840Ppiq9a_mprepulse inhibition QTL 9a (mouse)115249438586494385Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
1300664Etohcta9_methanol conditioned taste aversion 9 (mouse)Not determined115775466091754758Mouse
10053682Eae45_mexperimental allergic encephalomyelitis susceptibility 45 (mouse)Not determined115849055574754758Mouse
10053687Eae6_msusceptibility to experimental allergic encephalomyelitis 6 (mouse)Not determined111778196668500330Mouse
1300924Ity2_mimmunity to S. typhimurium 2 (mouse)Not determined15850803087695238Mouse
13208569Bmiq10_mbody mass index QTL 10 (mouse)113589082784890826Mouse
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
4141582Lgaq1_mlate growth adjusted QTL 1 (mouse)Not determined1226863768500330Mouse
4141966Tailq1_mtail length QTL 1 (mouse)Not determined1226863768500330Mouse
11532699Sluc36b_msusceptibility to lung cancer 36b (mouse)114225661776256730Mouse
11532698Sluc36a_msusceptibility to lung cancer 36a (mouse)114225661776256730Mouse
1300774Pgia7_mproteoglycan induced arthritis 7 (mouse)Not determined115339058887390737Mouse
1558945Orgwq8_morgan weight QTL 8 (mouse)Not determined111705617567078411Mouse
11532697Sluc36_msusceptibility to lung cancer 36 (mouse)115925661769482699Mouse
4142216Lgq1_mlate growth QTL 1 (mouse)Not determined1226863768500330Mouse
1302186Blmpf2_mbleomycin-induced pulmonary fibrosis 2 (mouse)Not determined115406567067078411Mouse
4141830Pregq1_mpregnancy QTL 1 (mouse)Not determined115412675283733652Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
13524848Ppiq7_mprepulse inhibition QTL 7 (mouse)112856914762569147Mouse
1357782Char8_mP. chabaudi malaria resistance QTL 8 (mouse)Not determined113557861669684987Mouse
39128214Lwq20_mliver weight QTL 20 (mouse)1112268637118022724Mouse
11059563Lmr31_mleishmaniasis resistance 31 (mouse)113210057766100694Mouse
1301328Mol4_mmodifier of LPS-response 4 (mouse)Not determined113628257783481356Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
1559002Lmrq4_mLeishmania major resistance QTL 4 (mouse)Not determined111226863769684947Mouse
1301830Ssta4_msusceptibility to Salmonella typhimurium antigens 4 (mouse)Not determined115007819184078411Mouse
4142308W6q3_mweight 6 weeks QTL 3 (mouse)Not determined111226863768500330Mouse
1357640Orq2_movulation rate QTL 2 (mouse)Not determined111226863768500330Mouse
10766457Nwa3_mNew Zealand White autoimmunity 3 (mouse)113801611572016209Mouse
4142300Ctrq3_mC. trachomatis resistance QTL 3 (mouse)Not determined114463003876854757Mouse
1357437Epfq4_mepididymal fat pad weight QTL 4 (mouse)Not determined111226863768500330Mouse
27226738Metcl11_mmetatarsal-calcaneal length 11, 10 week (mouse)11885000061390826Mouse
11522752Cocia18_mcocaine-induced activity, QTL 18 (mouse)113100820965008209Mouse
1301988Bmd11_mbone mineral density 11 (mouse)Not determined114631940780319522Mouse
4141127W3q4_mweight 3 weeks QTL 4 (mouse)Not determined1226863768500330Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
4142148Ckdbp2_mchronic kidney disease blood pressure locus 2 (mouse)Not determined115408094165103841Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse

Markers in Region
RH128681  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381160,788,031 - 60,788,220UniSTSGRCm38
MGSCv371160,601,533 - 60,601,722UniSTSGRCm37
Cytogenetic Map11B2UniSTS
AI642055  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381160,787,892 - 60,788,039UniSTSGRCm38
MGSCv371160,601,394 - 60,601,541UniSTSGRCm37
Cytogenetic Map11B2UniSTS
Whitehead/MRC_RH11801.97UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000056907   ⟹   ENSMUSP00000055926
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1160,668,351 - 60,679,113 (+)Ensembl
GRCm38.p6 Ensembl1160,777,525 - 60,788,287 (+)Ensembl
Ensembl Acc Id: ENSMUST00000102667   ⟹   ENSMUSP00000099728
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1160,668,350 - 60,671,893 (+)Ensembl
GRCm38.p6 Ensembl1160,777,524 - 60,781,067 (+)Ensembl
RefSeq Acc Id: NM_001085440   ⟹   NP_001078909
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391160,668,351 - 60,679,113 (+)NCBI
GRCm381160,777,525 - 60,788,287 (+)ENTREZGENE
MGSCv371160,591,027 - 60,601,789 (+)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_175491   ⟹   NP_780700
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391160,668,351 - 60,671,893 (+)NCBI
GRCm381160,777,525 - 60,781,067 (+)NCBI
MGSCv371160,591,027 - 60,601,789 (+)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_780700   ⟸   NM_175491
- Peptide Label: isoform 2
- UniProtKB: Q3UMB5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001078909   ⟸   NM_001085440
- Peptide Label: isoform 1
- UniProtKB: Q3UMB5 (UniProtKB/Swiss-Prot),   Q8BNG6 (UniProtKB/Swiss-Prot),   Q5U4H2 (UniProtKB/Swiss-Prot),   Q8C704 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000055926   ⟸   ENSMUST00000056907
Ensembl Acc Id: ENSMUSP00000099728   ⟸   ENSMUST00000102667
Protein Domains
cDENN FLCN/SMCR8-type   dDENN FLCN/SMCR8-type   uDENN FLCN/SMCR8-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3UMB5-F1-model_v2 AlphaFold Q3UMB5 1-935 view protein structure

Promoters
RGD ID:6822172
Promoter ID:MM_KWN:7741
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000101115,   ENSMUST00000117743,   ENSMUST00000120417,   NM_001085440,   NM_175491,   OTTMUST00000017705,   OTTMUST00000017707,   UC007JGM.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361160,590,121 - 60,595,002 (+)MPROMDB
RGD ID:8674896
Promoter ID:EPDNEW_M15479
Type:multiple initiation site
Name:Smcr8_1
Description:Mus musculus Smith-Magenis syndrome chromosome region, candidate8 homolog , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381160,777,538 - 60,777,598EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2444720 AgrOrtholog
Ensembl Genes ENSMUSG00000049323 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000056907 ENTREZGENE
  ENSMUST00000056907.7 UniProtKB/Swiss-Prot
  ENSMUST00000102667 ENTREZGENE
  ENSMUST00000102667.5 UniProtKB/Swiss-Prot
InterPro FLCN/SMCR8_DENN UniProtKB/Swiss-Prot
  Folliculin/SMCR8_N UniProtKB/Swiss-Prot
KEGG Report mmu:237782 UniProtKB/Swiss-Prot
MGD MGI:2444720 ENTREZGENE
NCBI Gene 237782 ENTREZGENE
PANTHER GUANINE NUCLEOTIDE EXCHANGE PROTEIN SMCR8 UniProtKB/Swiss-Prot
  SMITH-MAGENIS SYNDROME REGION GENE 8 PROTEIN UniProtKB/Swiss-Prot
Pfam Folliculin UniProtKB/Swiss-Prot
PhenoGen Smcr8 PhenoGen
PROSITE DENN_FLCN_SMCR8 UniProtKB/Swiss-Prot
UniProt Q3UMB5 ENTREZGENE
  Q5U4H2 ENTREZGENE
  Q8BNG6 ENTREZGENE
  Q8C704 ENTREZGENE
  SMCR8_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q5U4H2 UniProtKB/Swiss-Prot
  Q8BNG6 UniProtKB/Swiss-Prot
  Q8C704 UniProtKB/Swiss-Prot